4FL4 | pdb_00004fl4

Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FL4

This is version 1.3 of the entry. See complete history

Literature

Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome.

Currie, M.A.Adams, J.J.Faucher, F.Bayer, E.A.Jia, Z.Smith, S.P.

(2012) J Biological Chem 287: 26953-26961

  • DOI: https://doi.org/10.1074/jbc.M112.343897
  • Primary Citation Related Structures: 
    4FL4

  • PubMed Abstract: 

    Cellulosomes are multienzyme complexes responsible for efficient degradation of plant cell wall polysaccharides. The nonenzymatic scaffoldin subunit provides a platform for cellulolytic enzyme binding that enhances the overall activity of the bound enzymes. Understanding the unique quaternary structural elements responsible for the enzymatic synergy of the cellulosome is hindered by the large size and inherent flexibility of these multiprotein complexes. Herein, we have used x-ray crystallography and small angle x-ray scattering to structurally characterize a ternary protein complex from the Clostridium thermocellum cellulosome that comprises a C-terminal trimodular fragment of the CipA scaffoldin bound to the SdbA type II cohesin module and the type I dockerin module from the Cel9D glycoside hydrolase. This complex represents the largest fragment of the cellulosome solved by x-ray crystallography to date and reveals two rigid domains formed by the type I cohesin·dockerin complex and by the X module-type II cohesin·dockerin complex, which are separated by a 13-residue linker in an extended conformation. The type I dockerin modules of the four structural models found in the asymmetric unit are in an alternate orientation to that previously observed that provides further direct support for the dual mode of binding. Conserved intermolecular contacts between symmetry-related complexes were also observed and may play a role in higher order cellulosome structure. SAXS analysis of the ternary complex revealed that the 13-residue intermodular linker of the scaffoldin subunit is highly dynamic in solution. These studies provide fundamental insights into modular positioning, linker flexibility, and higher order organization of the cellulosome.


  • Organizational Affiliation
    • Department of Biomedical and Molecular Sciences, University, Kingston, Ontario K7L 3N6, Canada.

Macromolecule Content 

  • Total Structure Weight: 266.85 kDa 
  • Atom Count: 16,313 
  • Modeled Residue Count: 2,156 
  • Deposited Residue Count: 2,384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 9
A, D, G, J
88Acetivibrio thermocellusMutation(s): 0 
Gene Names: Cther_2220
EC: 3.2.1.4
UniProt
Find proteins for A3DDN1 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DDN1 
Go to UniProtKB:  A3DDN1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DDN1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Scaffolding dockerin binding protein A
B, E, H, K
187Acetivibrio thermocellusMutation(s): 0 
Gene Names: sdbA
UniProt
Find proteins for P71143 (Acetivibrio thermocellus)
Explore P71143 
Go to UniProtKB:  P71143
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71143
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellulosome anchoring protein cohesin region
C, F, I, L
321Acetivibrio thermocellusMutation(s): 0 
Gene Names: ClothDRAFT_2952
UniProt
Find proteins for Q46453 (Acetivibrio thermocellus)
Explore Q46453 
Go to UniProtKB:  Q46453
Entity Groups
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UniProt GroupQ46453
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
BB [auth H]
BC [auth L]
CA [auth C]
AA [auth C],
BA [auth C],
BB [auth H],
BC [auth L],
CA [auth C],
CB [auth H],
CC [auth L],
DB [auth H],
DC [auth L],
EB [auth H],
EC [auth L],
FA [auth E],
FB [auth H],
FC [auth L],
GA [auth E],
GB [auth H],
GC [auth L],
HA [auth E],
HB [auth H],
HC [auth L],
IA [auth E],
JA [auth E],
KA [auth E],
KB [auth I],
LA [auth E],
LB [auth I],
MB [auth I],
NB [auth I],
O [auth B],
OA [auth F],
OB [auth I],
P [auth B],
PA [auth F],
PB [auth I],
Q [auth B],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
SB [auth K],
T [auth B],
TA [auth F],
TB [auth K],
UA [auth F],
UB [auth K],
VA [auth F],
VB [auth K],
W [auth C],
WA [auth F],
WB [auth K],
X [auth C],
XA [auth F],
XB [auth K],
Y [auth C],
YA [auth F],
YB [auth K],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
AB [auth G]
AC [auth L]
DA [auth D]
EA [auth D]
IB [auth I]
AB [auth G],
AC [auth L],
DA [auth D],
EA [auth D],
IB [auth I],
JB [auth I],
M [auth A],
MA [auth F],
N [auth A],
NA [auth F],
QB [auth J],
RB [auth J],
U [auth C],
V [auth C],
ZA [auth G],
ZB [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.374α = 90
b = 186.305β = 90
c = 191.165γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references
  • Version 1.2: 2012-08-22
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations